ArticleJournal of proteome research2017
Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli.
Article in Journal of proteome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Genomic analysis of TIFY genes in two Medicago and insight into MsTF2-mediated abiotic stress tolerance.Plant cell reports · 2026Article
- Less missing values-evaluation of proteomics workflows for the quantification of (small) proteins.microLife · 2026Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Microproteins unveiling new dimensions in cancer.Functional & integrative genomics · 2024Review
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides.Biochemical Society transactions · 2023Review
- A frameshift ineLife · 2023Article
- Rescue ofeLife · 2023Article
- Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.PLoS genetics · 2021Article
- Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines.Journal of proteome research · 2020Article
- Non-AUG start codons: Expanding and regulating the small and alternative ORFeome.Experimental cell research · 2020Review
- Review
- Alternative ORFs and small ORFs: shedding light on the dark proteome.Nucleic acids research · 2020Review
- Proteomic Detection and Validation of Translated Small Open Reading Frames.Current protocols in chemical biology · 2019Article
- Small open reading frames and cellular stress responses.Molecular omics · 2019Review
- Unraveling the hidden universe of small proteins in bacterial genomes.Molecular systems biology · 2019Article
- Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein.Biochemistry · 2018Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances in mass spectrometry-based proteomics have revealed translation of previously nonannotated microproteins from thousands of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes. Facile methods to determine cellular functions of these newly discovered microproteins are now needed. Here, we couple semiquantitative comparative proteomics with whole-genome database searching to identify two nonannotated, homologous cold shock-regulated microproteins in Escherichia coli K12 substr. MG1655, as well as two additional constitutively expressed microproteins. We apply molecular genetic approaches to confirm expression of these cold shock proteins (YmcF and YnfQ) at reduced temperatures and identify the noncanonical ATT start codons that initiate their translation. These proteins are conserved in related Gram-negative bacteria and are predicted to be structured, which, in combination with their cold shock upregulation, suggests that they are likely to have biological roles in the cell. These results reveal that previously unknown factors are involved in the response of E. coli to lowered temperatures and suggest that further nonannotated, stress-regulated E. coli microproteins may remain to be found. More broadly, comparative proteomics may enable discovery of regulated, and therefore potentially functional, products of smORF translation across many different organisms and conditions.
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Registered trials
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